Everything is "unconfigured" after upgrades

We ran into a similar issue where the url worked correctly for accessing the Jazz Server, but when we used the same address with the RTC Eclipse client we ran into issues.  It seems like the RTC Eclipse client was not able to ignore the use of the proxy where the Internet Explorer use was able to ignore the proxy.  This is programmable in both Internet Explorer and in RTC Eclipse.  When we changed the network connection type from "Native" to "Direct", we were able to connect directly to our server and not have the proxy interfere with access.

When you mention "everything", you mean that all project areas are showing as "unconfigured" ?
Are you using Master/Child Project Areas ? Could be that the Master Project Area was missed ?
I do recommend you open a Support Request (PMR) to investigate this.

And using Web UI ? Are you able to see the configuration ?

Wondering if you are not facing any kind of connection issue on your Eclipse x CCM. Check your <workspace directory>/.metadata/.log file if there is any significant error being logged at the time you had opened the configuration.

Check your network connection configuration -

go to:
Windows > Preferences > Network Connection setting in the eclipse client

If it is using native and you do not have other entries except localhost in the proxy section, change it to direct.

Stop eclipse, clean the %temp% directory (For example: C:\Documents and Settings\<user>\Local Settings\Temp) and start Eclipse using a new Workspace.

I figured out the cause, though not the reason. If I copy the jdk folder from the "RTC official client" folder and add the following to my eclipse.ini file for Luna, it works fine:

-vm
jdk\jre\bin

I did try setting -vm to the java 8 bin folder, but that didn't help. This is the first time in 4 years I've had a problem using the "latest java" with RTC. We need to keep our machines updated to the latest java for security reasons. In fact, we have programs that do a security check and won't run if we're behind on java.

It appears RTC 5.0.2 does not work with Java 8 u25 (at least not 64 bit), even though RTC 4.0.6 and 5.0.1 work just fine with it. And it does appear to work for 15 seconds and then fail, which is especially weird. And most of the tool continues to work fine - just the project configuration fails to function.